3g Upgrade Plug Question

I stated earlier that i had the yellow/ white connected like stock from "D" plug(way #2)
then i tried the yellow/white loop PA style (way #3)
so i've done both ways.
i will go back to the stock wiring and recheck loads.
did check that yellow/white stock wiring and it did get 12.65v at Atl plug, so fuse is good.

Ok here's the retest numbers with yellow/white back on the "D" plug along original stock wiring harness.

Engine off:
Battery + - = 12.65v
Alt stud = 12.65v

Engine at idle:
battery + - = 14.44v
Alt stud = 14.64v

Engine @ idle(750 rpm with e-cam) with lights and all accessories on high:
Battery : 13v
Alt stud : 13.33v

Engine @ 2000 rpm with lights and all accessories on high
Battery = 14.45v
Alt stud = 14.65v

Beginning to think this is just another issue other than an Alternator problem.
In neutral I control rev it slow, perfect sound, timing, idle etc
When I turn on the head lights or turn on the a/c controls while doing the slow control rev
it skips or hesitates around 3000-3500 rpms.
With radio playing it does not skip or hesitate either.
Fuel pressure doesn't change, no drop, spike etc during the skip or misfire.
Have a new billet MSD distributor 7months old, MSD coil 7 months old, spark plugs and wires are a couple months old, they still look fine,
no cracks in the boots. cap/rotor look good as well.
New fuel filter 1 day old, walbro 25ol pump 7 months old

Put a new stock coil on and the skip drops to 2000-2500 rpms with the lights and all on.
No codes, starts up fine, idles perfect.

Maybe a TPS problem, I'll get some readings when I can.

Don't have either to test but I pulled my plugs and they look like toothpicks on the center electrode.